Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Zhang, Xue Song

doi:10.1128/jb.00113-12

Cited by 23 publications

(25 citation statements)

References 58 publications

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“…Allelic diversity in restriction modification (RM) systems represents a potential cause. In H. pylori, RM systems antagonize natural transformation (63,64). Several RM systems have been identified in S. pneumoniae strains, including type I (e.g., Spn556II/SpnD39III and Spn556III) and type II (e.g., Dpn and Spn556I/SpnD39I) systems (65)(66)(67).…”

Section: Discussionmentioning

confidence: 99%

Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence

et al. 2016

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h Natural genetic transformation of Streptococcus pneumoniae, an important human pathogen, mediates horizontal gene transfer for the development of drug resistance, modulation of carriage and virulence traits, and evasion of host immunity. Transformation frequency differs greatly among pneumococcal clinical isolates, but the molecular basis and biological importance of this interstrain variability remain unclear. In this study, we characterized the transformation frequency and other associated phenotypes of 208 S. pneumoniae clinical isolates representing at least 30 serotypes. While the vast majority of these isolates (94.7%) were transformable, the transformation frequency differed by up to 5 orders of magnitude between the least and most transformable isolates. The strain-to-strain differences in transformation frequency were observed among many isolates producing the same capsule types, indicating no general association between transformation frequency and serotype. However, a statistically significant association was observed between the levels of transformation and colonization fitness/virulence in the hypertransformable isolates. Although nontransformable mutants of all the selected hypertransformable isolates were significantly attenuated in colonization fitness and virulence in mouse infection models, such mutants of the strains with relatively low transformability had no or marginal fitness phenotypes under the same experimental settings. This finding strongly suggests that the pneumococci with high transformation capability are "addicted" to a "hypertransformable" state for optimal fitness in the human host. This work has thus provided an intriguing hint for further investigation into how the competence system impacts the fitness, virulence, and other transformation-associated traits of this important human pathogen. Streptococcus pneumoniae (the pneumococcus) is a commensal in the upper airway of humans and an opportunistic pathogen for numerous infections, including pneumonia, otitis media, and meningitis (1). Genetic plasticity of S. pneumoniae mediated by horizontal gene transfer is a primary driving force behind the success of this pathogen in its adaptation to the increasingly hostile environment in humans, the only known natural host (2). S. pneumoniae is capable of horizontal gene transfer via transduction, transformation, conjugation, and specialized transduction (or pseudotransduction) (3). Natural genetic transformation, referred to as natural transformation herein, alters the bacterial genome via uptake of foreign DNA and subsequent integration of new sequences into recipient genomes by homologous recombination (4). Although natural transformation appears to be the sole mechanism of transferring chromosomal DNA in S. pneumoniae, conjugation mobilizes the transfer of integrative and conjugative elements (ICEs) between pneumococcal cells or between S. pneumoniae and other Gram-positive bacteria (3).Natural transformation has been attributed to the acquisition of exogenous genes for immune ev...

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Section: Discussionmentioning

confidence: 99%

Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence

et al. 2016

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“…Helicobacter pylori J99 was originally isolated by Blaser lab from an American patient with duodenal ulcer 2 and sequenced in 1999 3 . H. pylori cells (50 μl) of J99 frozen stock from Blaser lab were first spotted on trypticase soy agar (TSA) plates with 5% sheep blood (TSA, BBL Microbiology Systems, Cockeysville, MD) at 37°C with 5% CO2 for 48-hour incubation, and then spread on new TSA plates in the same conditions 4 . After 24-h incubation, H. pylori cells were collected in 1.0 mL phosphate-buffered saline (PBS, pH 7.4), and centrifuged at 800 g for 5 min.…”

Section: Methodsmentioning

confidence: 99%

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

Beaulaurier

Zhu

Sebra

et al. 2014

Preprint

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Comprehensive genome-wide analyses of bacterial DNA methylation have not been possible until the recent advent of single molecule, real-time (SMRT) sequencing.This technology enables the direct detection of N6-methyladenine (6mA) and 4-methylcytosine (4mC) at single nucleotide resolution on a genome-wide scale. The distributions of these two major types of DNA methylation, along with 5-methylcytosine (5mC), comprise the bacterial methylome, some rare exceptions notwithstanding. SMRT sequencing has already revealed marked diversity in bacterial methylomes as well as the existence of heterogeneity of methylation in cells in single bacterial colonies, where such 'epigenetic' variation can enable bacterial populations to rapidly adapt to changing conditions. However, current methods for studying bacterial methylomes using SMRT sequencing mainly rely on population-level summaries that do not provide the single-cell resolution necessary for dissecting the epigenetic heterogeneity in bacterial populations. Here, we present a novel SMRT sequencing-based framework, consisting of two complementary methods, for single molecule-level detection of DNA methylation and assessment of methyltransferase activity through single molecule-level long read-based epigenetic phasing. Using seven bacterial strains and integrating data from SMRT and Illumina sequencing, we show that our method yields significantly improved resolution compared to existing population-level methods, and reveals several distinct types of epigenetic heterogeneity. Our approach enables new investigations of the complex architecture and dynamics of bacterial methylomes and provides a powerful new tool for the study of bacterial epigenetic control.All rights reserved. No reuse allowed without permission.

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“…In H. pylori , Type II R–M systems act as the main barrier against natural transformation (15,16). A 30-fold higher transformation frequency was observed for DNA from other strains when four Type II restriction enzymes were deleted in H. pylori strain 26695 (17). The inter-strain transformation frequency is reduced but not completely blocked by R–M systems indicating its regulation during horizontal gene transfer (16).…”

Section: Introductionmentioning

confidence: 91%

Helicobacter pylori DprA alleviates restriction barrier for incoming DNA

Dwivedi

Sharma

Rao

2013

Nucleic Acids Research

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Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction–modification (R–M) systems in this bacterium creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural transformation of several Gram-positive and Gram-negative bacteria by protecting incoming single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring protection to both from various exonucleases and Type II restriction enzymes. Here, we observed a stimulatory role of HpDprA in DNA methylation through physical interaction with methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R–M systems by not only inhibiting the restriction enzymes but also stimulating methyltransferases. These results indicate that HpDprA could be one of the factors that modulate the R–M barrier during inter-strain natural transformation in H. pylori.

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Natural Transformation of an Engineered Helicobacter pylori Strain Deficient in Type II Restriction Endonucleases

Cited by 23 publications

References 58 publications

Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence

Addiction of Hypertransformable Pneumococcal Isolates to Natural Transformation for In Vivo Fitness and Virulence

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

Helicobacter pylori DprA alleviates restriction barrier for incoming DNA

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